int main(int argc, char **argv) {
std::cout<<"Usage: GetHOG3D image.vtk mesh.vtp label_array_name output_hog.csv output_label.csv radius"<<std::endl;
// const char* inputImageFileName = "/home/costa/Dropbox/code/HOG3D/bin/01D-LGE-320.vtk";
// const char* inputMeshFileName = "/home/costa/Dropbox/code/HOG3D/bin/01D_320_autolabels.vtp";
// const char* outputHogFileName = "/home/costa/Dropbox/code/HOG3D/bin/01D_320_hog.csv";
// const char* outputLabelsFileName = "/home/costa/Dropbox/code/HOG3D/bin/01D_320_lbl.csv";
// const char* labelArrayName = "autolabels";
if(argc<6) return EXIT_FAILURE;
int c=1;
const char* inputImageFileName = argv[c++];
const char* inputMeshFileName = argv[c++];
const char* labelArrayName = argv[c++];
const char* outputHogFileName = argv[c++];
const char* outputLabelsFileName = argv[c++];
float radius = atof(argv[c++]);
const int ngrad_bins = 8; //number of gradient orientation bins
//define some region of interest around the point
arma::vec radii;
radii << radius; //mm
//----------------------------------------------------
//
//
// read the image
//
//
typedef unsigned int PixelType;
typedef itk::Image< PixelType, 3 > ImageType;
typedef itk::ImageFileReader< ImageType > ImageReaderType;
typename ImageReaderType::Pointer imageReader = ImageReaderType::New();
imageReader->SetFileName(inputImageFileName);
try {
imageReader->Update();
} catch (itk::ExceptionObject& e) {
std::cerr << e.what() << std::endl;
return EXIT_FAILURE;
}
//
//
//----------------------------------------------------
//----------------------------------------------------
//
// read the mesh
//
//
//
vtkSmartPointer<vtkXMLPolyDataReader> rd = vtkSmartPointer<vtkXMLPolyDataReader>::New();
rd->SetFileName(inputMeshFileName);
rd->Update();
vtkPolyData* mesh = rd->GetOutput();
//calculate normals
vtkSmartPointer<vtkPolyDataNormals> ng = vtkSmartPointer<vtkPolyDataNormals>::New();
ng->SetInputData(mesh);
ng->SplittingOff();
ng->Update();
vtkDataArray* pnormals = ng->GetOutput()->GetPointData()->GetNormals();
//
//
//----------------------------------------------------
//----------------------------------------------------
//
// save the labels
//
//
//
std::cout<<"Saving the labels"<<std::endl;
vtkDataArray* mesh_labels = mesh->GetPointData()->GetArray(labelArrayName);
arma::uvec labels(mesh_labels->GetNumberOfTuples());
for(int i=0; i<mesh_labels->GetNumberOfTuples(); i++)
{
labels(i) = mesh_labels->GetTuple1(i);
}
labels.save(outputLabelsFileName, arma::raw_ascii);
//
//
//----------------------------------------------------
//----------------------------------------------------
//
// for each point of the mesh, take normal and
// for each scale (radius+sigma) get the HOG
//
//
//
//create the matrix to store everything
//every row - HOGS of one point
std::cout<<"Calculating HOGs"<<std::endl;
//sample something to know the size of the neighborhood
double pt[3];
mesh->GetPoint(0, pt);
arma::ivec samples;
SampleGradHistogram<ImageType>(pt, radii[0], imageReader->GetOutput(), samples);
arma::imat sample_matrix(mesh->GetNumberOfPoints(), samples.size());
const int nsamples = samples.size();
//
for(int j=0; j<radii.size(); j++)
{
std::cout<<"Radius "<<radii[j]<<std::endl;
for(int i=0; i<mesh->GetNumberOfPoints(); i++)
{
if(i%1000==0)
std::cout<<"Point "<<i<<"/"<<mesh->GetNumberOfPoints()<<"\r"<<std::flush;
double pt[3];
mesh->GetPoint(i, pt);
SampleGradHistogram<ImageType>(pt, radii[j], imageReader->GetOutput(), samples);
if(nsamples!=samples.size())
std::cout<<std::endl<<"Nonconstant number of samples (vertex "<<i<<"): "<<nsamples<<" vs "<<samples.size()<<std::endl<<std::flush;
//copy the histogram into the matrix
for(int k=0; k<samples.size(); k++)
{
sample_matrix(i,k) = samples(k);
}
}
std::cout<<std::endl;
}
//
//
//----------------------------------------------------
std::cout<<std::endl<<"Saving"<<std::endl;
//save the matrix
sample_matrix.save(outputHogFileName, arma::arma_binary);
//
return EXIT_SUCCESS;
}
shared_ptr<arma::mat> sample_matrix(gsl_rng* rng) {
return sample_matrix(rng, all_examples);
}
